SAGExplore

SAGExplore maps Serial Analysis of Gene Expression (SAGE) tags to genomic annotations to reduce ambiguous tag assignments and improve the precision of gene expression analysis.

Key Features:

• Genomic Virtual Tags Database: A comprehensive database of genomic virtual SAGE tags that provides a complete annotation of potential tags and estimates confidence for experimental observation to reduce ambiguous assignments.
• Tag Ranking by Observation Likelihood: Tags with multiple genomic matches are ranked by estimated confidence or likelihood of experimental observation to prioritize assignments.
• Accurate Mapping for Yeast: Optimized mapping of experimental SAGE tags against yeast genomic annotations to support gene expression analysis and discovery.
• Export Formats: Generates a tab-delimited text file of results for downstream analysis.
• Planned Expansion to Other Organisms: Intended extension to support mapping experimental SAGE tags from humans, mice, frogs, and flies.

Scientific Applications:

• Gene Expression Profiling: Mapping SAGE tags to genomic annotations to quantify gene expression from SAGE experiments.
• Gene Discovery and Annotation: Reducing ambiguous tag assignments to improve gene discovery and annotation derived from SAGE data.
• Interpretation of Non-Unique Tags: Prioritizing non-unique tags by confidence to enable more reliable interpretation of experimental SAGE observations.

Methodology:

Constructs a database of genomic virtual tags representing potential experimental observations and ranks tags by estimated likelihood of observation to minimize ambiguous non-unique tag assignments.